Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.

ABSTRACT: Experiments have suggested that ion correlation and fluctuation effects can be potentially important for multivalent ions in RNA folding. However, most existing computational methods for the ion electrostatics in RNA folding tend to ignore these effects. The previously reported tightly bound ion (TBI) model can treat ion correlation and fluctuation but its applicability to biologically important RNAs is severely limited by the low computational efficiency. Here, on the basis of Monte Carlo sampling for the many-body ion distribution, we develop a new computational model, the Monte Carlo tightly bound ion (MCTBI) model, for ion-binding properties around an RNA. Because of an enhanced sampling algorithm for ion distribution, the model leads to a significant improvement in computational effic

SUBMITTER: Sun LZ 

PROVIDER: S-EPMC5520805 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature